PROJECT SUMMARY For reasons that are not well understood, brain disorders are highly phenotypically variable and often the same gene is implicated in different disorders. To address these challenges, a deeper understanding of the mechanisms that regulate brain gene expression and brain cell development are required to set the stage for preventative interventions and personalized outcome prediction and therapies. Interactions between genetic and epigenetic effects could play important roles in shaping phenotypic variance and risk. In a recent paper in Neuron, we uncovered epigenetic allele-specific expression effects in the mouse, macaque and human brain. The data indicate that hundreds of genes differentially express their maternal and paternal alleles in vivo in a developmentally regulated manner; we refer to these effects as differential allele expression effects (DAEEs). DAEEs are not due to genetic variation or genomic imprinting, and involve random monoallelic expression at the cellular level. We show that DAEEs interact with heterozygous mutations to cause mosaics of monoallelic brain cells that differentially express mutant versus wildtype alleles. The results reveal a new layer of gene regulation at the allele and cellular level that can shape genetic architecture. Currently, we do not know the mechanistic basis of DAEEs in the brain. Here, we will test the hypothesis that DAEEs are caused by allele-specific inter- and intra- chromosomal regulatory contacts in the genome of brain cells. 3D genomic regulatory architecture has important roles in gene regulation and changes developmentally, but little is known about 3D regulatory architecture at the allele level in vivo in the brain. In Goal 1.1, we test whether DAEEs involve allele-specific regulatory contacts in the genome. This study will uncover new regulatory architecture at the allele level in the brain that could improve our understanding of the mechanisms causing phenotypic variance. In Goal 1.2, we will independently validate allelic regulatory contacts using double 3D Fluorescent In Situ Hybridization (FISH) in primary mouse brain cells. This study will independently confirm random monoallelic contact events in single brain cells. Overall, we expect to uncover the mechanistic basis of DAEEs and novel allele-specific features of gene regulation in the mouse brain genome. The results will set the foundation for future functional studies, and improve our understanding of how allele- specific epigenetic effects can arise in vivo and could influence phenotypic variance and brain disorder risks.